Rick Kesseli - Academia.edu (original) (raw)

Papers by Rick Kesseli

Springer eBooks, 1992

Conservation of rare and endangered plant taxa and their habitats requires an understanding of th... more Conservation of rare and endangered plant taxa and their habitats requires an understanding of the population dynamic factors affecting recruitment, reproduction, dispersal and genetic capacity to evolve. Population size, dispersion and certain genetic structure variables determining effective population size are reviewed in order to emphasize the maintenance of genetic variation in small, subdivided populations. Research on an annual plant genus, Limnanthes living in vernal pools as islands and containing several rare taxa, provided excellent examples of many of these genetic and demographic properties. Genetic variation patterns based on allozyme surveys appeared to fit an island model such that rarity based on narrow geographical range and highly localized gene flow clearly affected the patterns. Several other rare plant examples are also reviewed briefly in order to point out the critical population biological research needed for designing nature reserves and their monitoring or management strategies. Current research in conservation biology should advance the in situ approaches, and some basic field studies as outlined here; in most cases, even preliminary information on life history, genetic structure, gene flow, breeding system and population size variation would prove highly valuable.

Proceedings of the National Academy of Sciences of the United States of America, Nov 1, 1991

We developed bulked segregant analysis as a method for rapidly identifying markers linked to any ... more We developed bulked segregant analysis as a method for rapidly identifying markers linked to any specific gene or genomic region. Two bulked DNA samples are generated from a segregating population from a single cross. Each pool, or bulk, contains individuals that are identical for a particular trait or genomic region but arbitrary at all unlinked regions. The two bulks are therefore genetically dissimilar in

Genetics, Oct 1, 2003

An RFLP genomic subtraction was used to isolate male-specific sequences in the species Silene lat... more An RFLP genomic subtraction was used to isolate male-specific sequences in the species Silene latifolia. One isolated fragment, SLP2, shares similarity to a portion of the Activator (Ac) transposase from Zea mays and to related proteins from other plant species. Southern blot analysis of male and female S. latifolia genomic DNA shows that SLP2 belongs to a low-copy-number repeat family with two Y-linked copies. Screening of a S. latifolia male genomic library using SLP2 as a probe led to the isolation of five clones, which were partially sequenced. One clone contains two large open reading frames that can be joined into a sequence encoding a putative protein of 682 amino acids by removing a short intron. Database searches and phylogenetic analysis show that this protein belongs to the hAT superfamily of transposases, closest to Tag2 (Arabidopsis thaliana), and contains all of the defined domains critical for the activity of these transposases. PCR with genomic and cDNA templates from S. latifolia male, female, and hermaphrodite individuals revealed that one of the Y-linked copies is transcriptionally active and alternatively spliced. This is the first report of a transcriptionally active transposable element (TE) family in S. latifolia and the first DNA transposon residing on a plant Y chromosome. The potential activity and regulation of this TE family and its use for Y chromosome gene discovery is discussed.

Genetics, Jun 1, 1987

A detailed linkage map of lettuce was constructed using 53 genetic markers including 41 restricti... more A detailed linkage map of lettuce was constructed using 53 genetic markers including 41 restriction fragment length polymorphism (RFLP) loci, five downy mildew resistance genes, four isozyme loci and three morphological markers. The genetic markers were distributed into nine linkage groups and cover 404 cM which may be 25-30% of the lettuce genome. The majority (31 of 34) of the RFLP probes detected single segregating loci, although seven of these may have been homologous to further monomorphic loci. When several loci were detected by a single probe, the loci were generally linked, suggesting tandem duplications. One probe, however, detected loci in three linkage groups suggesting translocations. The five downy mildew resistance genes (Dm1, Dm3, Dm4, Dm5/8 and Dm13), segregating in the Calmar x Kordaat cross, represented each of the four resistance gene linkage groups. Dm5/8 is flanked by two cDNA loci, each located 10 cM away. These flanking markers will be used to study the source of variation in downy mildew genes and are also part our strategy to clone resistance genes.

An integrated map for lettuce comprising of 2,744 markers was developed from seven intra-and inte... more An integrated map for lettuce comprising of 2,744 markers was developed from seven intra-and inter-speciWc mapping populations. A total of 560 markers that segregated in two or more populations were used to align the individual maps. 2,073 AFLP, 152 RFLP, 130 SSR, and 360 RAPD as well as 29 other markers were assigned to nine chromosomal linkage groups that spanned a total of 1,505 cM and ranged from 136 to 238 cM. The maximum interval between markers in the integrated map is 43 cM and the mean interval is 0.7 cM. The majority of markers segregated close to Mendelian expectations in the intra-spe-ciWc crosses. In the two L. saligna £ L. sativa inter-speciWc crosses, a total of 155 and 116 markers in 13 regions exhibited signiWcant segregation distortion. Data visualization tools were developed to curate, display and query the data. The integrated map provides a framework for mapping ESTs in one core mapping population relative to phenotypes that segregate in other populations. It also provides large numbers of markers for marker assisted selection, candidate gene identiWcation, and studies of genome evolution in the Compositae.

Theoretical and Applied Genetics, Sep 8, 2007

Current Plant Science and Biotechnology in Agriculture, 1993

We are developing approaches for map-based cloning of disease resistance genes. Specificity betwe... more We are developing approaches for map-based cloning of disease resistance genes. Specificity between lettuce and its fungal pathogen, Bremia lactucae, is conditioned by an unambiguous gene-for-gene interaction. Classical genetics of host and pathogen has defined 13 resistance genes (Dm) and matching avirulence genes. The resistance genes are clustered in four regions. The current genetic map comprises 319 markers. We are now focusing on saturating the regions containing resistance genes with PCR-based markers using near-isogenic lines, bulked segregant analysis, and deletion mutants. We are also mapping many genes for disease resistance in lettuce to test whether they are all clustered. Random amplified polymorphic DNA (RAPD) markers are being converted to sequence characterized amplified region (SCAR) markers to provide reliable markers flanking each resistance locus. Recombinants selected from large populations are being used to order closely linked markers in the vicinity of resistance genes. We are developing long-range restriction maps around the Dm genes and analyzing recombinants for changes in the map to orientate the physical map relative to the genetic map and to determine the relationship between genetic and physical distance in the region. We are currently preparing various libraries for chromosome walking and will start isolating overlapping clones when a physically close marker has been confirmed.

Rhodora, 2006

Abstract The genetic diversity and structure of Quercus rubra L. (Red Oak) in five secondary popu... more Abstract The genetic diversity and structure of Quercus rubra L. (Red Oak) in five secondary populations regenerated on old pastures and five paired old-growth populations were compared to determine whether secondary populations may have lost genetic diversity present in the presettlement forest. Old-growth samples had significantly greater nuclear allelic richness than secondary stands at the four microsatellite, simple sequence repeat (SSR), markers tested, but there was no significant difference at three chloroplast SSRs. There was however tenfold greater differentiation (high FST) among secondary forests than among old-growth forests for the chloroplast loci, suggesting greater population isolation at the time of their founding. The young age class in secondary stands had significantly greater chloroplast allelic richness than the old age class, suggesting some recovery as the forest cover increased. Forest cover and patch size at peak deforestation was not correlated with allelic richness in secondary stands, but the power of this test was low. The current size of old-growth stands is, however, positively correlated with levels of genetic diversity. Results suggest that deforestation for agriculture may reduce genetic diversity of forest trees, particularly in the first generation after deforestation, but that some recovery of this diversity is likely in these patchy landscapes. Wind dispersed pollen flow may increase in these areas, but animal dispersed seed flow may be reduced.

Molecular Ecology Resources, 2013

Although the Compositae harbours only two major food crops, sunflower and lettuce, many other spe... more Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here, we have used next-generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium intybus, Echinacea angustifolia, Iva annua, Helianthus tuberosus, Dahlia hybrida, Leontodon taraxacoides and Glebionis segetum, as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium argentatum and Smallanthus sonchifolius. Illumina reads were assembled using Trinity, and 454 reads were assembled using MIRA and CAP3. We evaluated the coverage of the transcriptomes using BLASTX analysis of a set of ultra-conserved orthologs (UCOs) and recovered most of these genes (88-98%). We found a correlation between contig length and read length for the 454 assemblies, and greater contig lengths for the 454 compared with the Illumina assemblies. This suggests that longer reads can aid in the assembly of more complete transcripts. Finally, we compared the divergence of orthologs at synonymous sites (Ks) between Compositae crops and their wild relatives and found greater divergence when the progenitors were self-incompatible. We also found greater divergence between pairs of taxa that had some evidence of postzygotic isolation. For several more distantly related congeners, such as chicory and endive, we identified a signature of introgression in the distribution of Ks values.

Genetics, Aug 1, 2006

Comparative genomic studies among highly divergent species have been problematic because reduced ... more Comparative genomic studies among highly divergent species have been problematic because reduced gene similarities make orthologous gene pairs difficult to identify and because colinearity is expected to be low with greater time since divergence from the last common ancestor. Nevertheless, synteny between divergent taxa in several lineages has been detected over short chromosomal segments. We have examined the level of synteny between the model species Arabidopsis thaliana and species in the Compositae, one of the largest and most diverse plant families. While macrosyntenic patterns covering large segments of the chromosomes are not evident, significant levels of local synteny are detected at a fine scale covering segments of 1-Mb regions of A. thaliana and regions of ,5 cM in lettuce and sunflower. These syntenic patches are often not colinear, however, and form a network of regions that have likely evolved by duplications followed by differential gene loss.

Genetics, Aug 1, 1998

The segregation pattern of an 810-bp random amplified polymorphic DNA (RAPD) band in the F 1 and ... more The segregation pattern of an 810-bp random amplified polymorphic DNA (RAPD) band in the F 1 and backcross generations of a Silene dioica (L.) Clairv. family provides evidence that this molecular marker is located in the pseudoautosomal region (PAR) of the X and Y chromosomes. The marker was found through a combination of bulked segregant analysis (BSA) and RAPD techniques. Recombination rates between this pseudoautosomal marker and the differentiating portion of the Y chromosome are 15% in both generations. Alternative explanations involving nondisjunction or autosomal inheritance are presented and discussed. Chromosome counts provide evidence against the nondisjunction hypothesis, and probability calculations argue against the possibility of autosomal inheritance. This constitutes the first report of a pseudoautosomal DNA marker for plant sex chromosomes.

Journal of Heredity, Sep 1, 1981

A microslab isoelectric focusing gel is demonstrated, using single pollen grains from F, hybrids ... more A microslab isoelectric focusing gel is demonstrated, using single pollen grains from F, hybrids of Cucurbita species. When zymograms of these single pollen grains were stained to indicate the presence of acid phosphatase zones, it was seen that at least 11 out of 37, or 29.7 percent of such zones are controlled by loci that are transcribed in the microgametophyte. These results suggest that gametophytically transcribed loci may be fairly common and also that their investigation is now technically unchallenging.

American Journal of Botany, Jul 1, 1984

Gynodioecy in two populations of Limnanthes douglasii var. rosea was studied for its maintenance ... more Gynodioecy in two populations of Limnanthes douglasii var. rosea was studied for its maintenance requirements, role in population structure and its influence on the levels ofoutbreeding. The mode of inheritance of male sterility appeared to be nucleo-cytoplasmic, although the precise number of nuclear genes and dominance relationships could not be ascertained. Measurements on the plants sampled from natural stands and controlled experiments showed that male-steriles and their progeny had greater biomass and more flowers per plant than hermaphrodites, though these results varied with the environmental conditions. The hermaphrodites of gynodioecious populations had higher rates of selfing than the hermaphrodite individuals in populations lacking male sterility. Estimates of the inbreeding depression and homozygosity levels were also higher in gynodioecious populations. Variation in these parameters of breeding system and relative heterozygosis among populations may explain why male sterility has a restricted distribution, as theoretical models also predict rather specific conditions for this stable polymorphism. These data suggest that the advantage ofmale sterility is associated with lowered inbreeding depression. However, the potential ecological resource reallocation to the female function needs to be investigated. The fitness differences observed in this study between male-steriles and hermaphrodites appear inadequate to maintain the nucleo-cytoplasmic male sterility but could account for the observed frequencies (10-20%) ofmale-steriles in nature if the genetic system has evolved from a cytoplasmic system.

American Journal of Botany, Jun 1, 2007

Although fundamental to the study of invasion mechanisms, the relationship between mode of reprod... more Although fundamental to the study of invasion mechanisms, the relationship between mode of reproduction and plant invasion is not well understood. Fallopia japonica (Japanese knotweed), a highly aggressive invasive plant in both Europe and North America, serves as a model species for examining this relationship. In Britain, F. japonica var. japonica is a single female clone reproducing solely through vegetative growth or obligate hybridization with other Fallopia spp. In the U.S., however, there is more evidence for sexual reproduction. Here, simple sequence repeat (SSR) markers were developed, and three Massachusetts populations were sampled at regular intervals. The amount of sexual and clonal reproduction in each population was determined based on within-population genetic diversity. Clonal growth was apparent, but the populations together contained 26 genotypes and had evidence of sexual reproduction. One genotype that was present in all populations matched the single aggressive British clone of F. japonica var. japonica. Also, a potentially diagnostic marker for the F. sachalinensis genome provided evidence of inter-and intraspecific sexual reproduction and introgression. These differences observed in U.S. populations compared to European populations have significant implications for management of Fallopia spp. in the U.S. and underscore the importance of regional studies of invasive species.

Conservation Biology, Oct 1, 1995

: The diversity and population structure of potato landraces (Solanum spp.) within their center o... more : The diversity and population structure of potato landraces (Solanum spp.) within their center of domestication was studied using isozyme surveys of four polymorphic loci. The objective in assessing the distribution of genetic diversity was to assist in planning conservation strategies of crop genetic resources that are threatened by genetic erosion. In situ conservation methods depend on this type of analysis. Research was conducted in the region of Cusco, Peru. Eight fields spread among two microregions were randomly sampled, and 610 tubers were studied from this sample. In addition, 503 tubers were collected from markets in seven different meso‐regions (provinces) surrounding the regional center of Cusco. Thirty genotypes were identified in the field sample and 82 in the regional sample. The frequency and distribution of genotypes and alleles are described. A high degree of genotype endemism was found at both the field and regional levels. Genotypes were unevenly distributed, and most of the genotypic diversity was between rather than within populations. At the allele level, however, we found that a very high percentage of the diversity was within rather than between populations. The genotype is the key unit for maintaining the population of potato landraces. Our findings suggest that collections need to be both geographically extensive and intensive. Because farmers are able to maintain most alleles on relatively small portions of their land, in situ conservation is a viable strategy.

… leafy vegetables 2003 …, 2003

The Compositae Genome Project (CGP) is in its third year. The initial phase has focused on sequen... more The Compositae Genome Project (CGP) is in its third year. The initial phase has focused on sequencing of expressed sequence tag (ESTs). Over 19 000 unigenes of lettuce have been identified, probably representing at least a third of all genes expressed in ...

Molecular Genetics and Genomics, Jun 14, 2008

The natural history of introduced species is often unclear due to a lack of historical records. E... more The natural history of introduced species is often unclear due to a lack of historical records. Even when historical information is readily available, important factors of the invasions such as genetic bottlenecks, hybridization, historical relationships among populations and adaptive changes are left unknown. In this study, we developed a set of nuclear, simple sequence repeat markers and used these to characterize the genetic diversity and population structure among native (Eurasian) and non-native (North and South American) populations of Centaurea solstitialis L., (yellow starthistle). We used these data to test hypotheses about the invasion pathways of the species that were based on historical and geographical records, and we make inferences about historical relationships among populations and demographic processes following invasion. We confirm that the center of diversity and the native range of the species is likely the eastern Mediterranean region in the vicinity of Turkey....